Command-line Tool

The Apache Taverna Command-line Tool is a script that runs Taverna workflows from a terminal. The command-line script is called executeworkflow (executeworkflow.bat on Windows and on Linux/UNIX).

You can download the Command-line Tool from the Taverna Web site or use the or executeworkflow.bat that is bundled with the Taverna Workbench installation.


What are the differences between the bundled and unbundled versions?

Other important information

Executeworkflow Script

Basic Operations

Running the script with a database


What are the differences between the bundled and standalone versions?

This section describes some of the differences between the bundled and standalone versions of *executeworkflow * Other important information is provided in the following section.

Other important information

This section provides additional information on configuring proxy settings, installing service plugins, disk space considerations and potential conflicts.

Executeworkflow Script

To get help and a full set of options for the executeworkflow script, type the following at the command prompt:

$ sh -help

This command will list the following usage options:

usage: executeworkflow [options] [workflow]

 -clientserver                                  Connects as a client to a
                                                Derby server instance.

 -cmdir <Credential Manager's directory path>   Absolute path to the
                                                directory on the disk
                                                where Credential Manager's
                                                files are located.

 -cmpassword                                    Indicates that the master
                                                password for Credential
                                                Manager will be provided
                                                on standard input.

 -dbproperties <filename>                       Loads a properties file to
                                                configure the database.

 -embedded                                      Connects to an embedded
                                                Derby database. This can
                                                prevent multiple

 -help                                          Displays comprehensive
                                                help information.

 -inmemory                                      Runs the workflow with
                                                data stored in-memory
                                                rather than in a database.
                                                This can give performance
                                                improvements, at the cost
                                                of overall memory usage.

 -inputdelimiter <inputname delimiter>          Causes an inputvalue or
                                                inputfile to be split into
                                                a list according to the
                                                delimiter. The associated
                                                workflow input must be
                                                expected to receive a list.

 -inputdoc <document>                           Loads inputs from a Baclava

 -inputfile <inputname filename>                Loads the named input from
                                                file or URL.

 -inputvalue <inputname value>                  Directly uses the value for
                                                the named input.

 -janus <file>                                  Saves Janus RDF/XML trace
                                                of execution to FILE or

 -logfile <filename>                            Creates logfile to which more
                                                verbose logging will be

 -opm <file>                                    Saves Open Provenance
                                                Model (OPM) RDF/XML trace
                                                of execution to FILE or

 -outputdir <directory>                         Save output as files in
                                                directory. Default is to
                                                make a new directory

 -outputdoc <document>                          Saves output to a new
                                                Baclava document.

 -port <portnumber>                             Returns port number that
                                                database is running on.
                                                If set requested to start its own
                                                internal server, this is
                                                the start port that will
                                                be used.

 -provenance                                    Generates provenance
                                                information and stores it
                                                in the database.

 -startdb                                       Automatically starts an
                                                internal Derby database


Basic Operations

This section describes inputs, outputs, and creating lists.

Creating or exporting files and directories

If this directory already exists, then a new directory is created and appended with _<n>, where n is incremented to the next available index.

Results are written to files named after the output port for that result. If a result is composed of lists, then a directory is created for the output port and individual list items are named after the list element index (with 1 being the first index). If the output is the result of an error, the filename is appended with ‘.error’.

You can provide your own output directory with the -outputdir option. (There will be an error if the directory already exists.)

You can export provenance using the -opm or -janus options.

You can also record your results to a Baclava document using -outputdoc option. The document will be overwritten if it already exists. (You can use the DataViewer Tool to view Baclava files.)

Inputting data

Inputs can be provided in three ways.

Creating a list

If one or more of your workflow inputs is described as a list, you can create a list using the -inputdelimiter option. This option may be used with either -inputfile or -inputvalue.

The -inputdelimiter option takes two parameters: an input name and the delimiter used to split the input into a list. The delimiter may be a simple character, such as a comma or a new-line character, or a regular expression. The input string (or file) will then be converted into a list using the specified delimiter.

If a list of greater depth is required (i.e., a list or lists or deeper) then you will need to use the -inputdocoption to pass data from a Baclava file. However, if you provide an input of lower depth than what is required, it will automatically be wrapped in one or more list levels up to the required depth. Providing an input of greater depth than that required will result in an error.

Running the script with a database

Storing data in memory is the default option. If a workflow has a high memory requirement, then it may be better to store data in a database. There are three options for using a database:

Advanced database operations

Advanced database configurations can be specified using the -dbproperties option, allowing you to take full control over the database used. This takes a second argument, the filename of the properties file. Below are the default settings for the properties file.

in_memory = true
provenance = false
connector = derby
port = 1527
dialect = org.hibernate.dialect.DerbyDialect
start_derby = false
driver = org.apache.derby.jdbc.EmbeddedDriver
jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true

Use Derby

If you want to run the Derby database with client/server setting instead of with the embedded driver, change the properties in the -dbproperties file (described above) as follows:


If you want to run your own separate Derby server instance, then do not define the start_derby option and instead define your Derby server port as port=<port>.


If you want to use MySQL rather than Derby, first copy the mysql-connector-java-5.1.5.jar file from the mySQL website into the lib folder of the Taverna installation directory. (The Taverna installation directory is where you are running the script.)

Edit the -dbproperties file as follows:


Important: The database name in the jdbcuri property must be T2Provenance, as this database name is hard-coded into the MySQL provenance SQL queries.

If you do not specify the port, the script will try to connect to the default port for MySQL server, which is 3306.

When using -dbproperties together with other options, the other options take precedence.


Workflows names are listed at the end of the command, after any options. You must enclose file paths and input values in quotes if they contain spaces. Examples are shown below.

Example 1

$ sh "/Users/alex/Taverna Workflows/wf-1.t2flow"

The command in Example 1 executes the workflow located in /Users/alex/Taverna Workflows/wf-1.t2flow. It has no input values and uses memory for data storage (the default option). Because no output directory is specified, a subdirectory for output files (<workflowName>_outputdirectory) will be created under the current directory.

Example 2

$ sh -embedded -inputvalue in1 aaa -inputvalue in2 "bb b" -outputdir /tmp/wf-2/ wf-2.t2flow

The command in Example 2 executes the workflow wf-2.t2flow from the current directory and uses the embedded Derby database to store the data. It passes the value “aaa” to input port in1 and the value “bb b” to input port in2. Output files will be written to the /tmp/wf-2/ directory.

Example 3

$ sh -inputvalue in1 aaa -inputfile in2 input2.txt -inputdelimiter in2 "\n" wf-3.t2flow

The command in Example 3 executes the workflow wf-3.t2flow from the current directory, passing the value “aaa” to input port in1. It splits the contents of file input2.txt using “\n” (new line character) as the delimiter and passes the resulting list to input port in2. NOTE: The delimiter must be in quotes, even if it is a single character, such as “;”. The <workflowName>_outputdirectory subdirectory will be created under the current directory and will contain all output files.

Example 4

$ sh -inputdoc /tmp/input-doc.xml -outputdoc /tmp/output-doc.xml "/Users/alex/Taverna Workflows/wf-4.t2flow"

The command in Example 4 executes the workflow /Users/alex/Taverna Workflows/wf-4.t2flow, loading inputs from the Baclava document in /tmp/input-doc.xml, and creating a Baclava document in the output directory: /tmp/output-doc.xml.